You can indeed reinstall phpmyadmin at any time you like. Should not affect the rest of the services.
If you suspect its your phpmyadmin install, you could use a second deployment to test - why not add a virtual host to your dns and ispconfig as a separate website, and deploy phpmyadmin into there.
For example, phptools.yourdomain.com
- add A host dns entries pointing to your server
- create ispconfig webiste site for domain
- download phpmyadmin and unpack to web folder, set file permissions as necessary
- run install script to generate config file and save
- access that copy of phpmyadmin by http(s)://phptools.yourdomain.com
- perhaps if you wanted simple added security password protect the folder you put it in.
If that installation works, you've got a problem with the original and you could compare things like config files, permissions, etc. If it doesnt work you might have another issue manifesting itself.
You can wipe the virtual site once you've completed your testing.